RetrogeneDB ID:

retro_btau_1741

Retrocopy
location
Organism:Cow (Bos taurus)
Coordinates:X:46306625..46308190(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSBTAG00000022306
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:GLUD1
Ensembl ID:ENSBTAG00000007540
Aliases:GLUD1, GDH
Description:Glutamate dehydrogenase 1, mitochondrial [Source:UniProtKB/Swiss-Prot;Acc:P00366]


Retrocopy-Parental alignment summary:






>retro_btau_1741
GGGCAGCATGCTGCAGCCATCAGTGCCCTGCAGCCAGGGCTTGTGCCATCCGCTCAGTGACACTACAGCGAGGTGGTGGC
CAACTGCGAGGATGACCTCAGCTTCTTCAATATGGTGGAGGGCTTCTTCGACCGTAGTGCCAGCATCATGGAGGACAAGC
TGGTGGAGGACCTCAAGACCCAGGAGACCGAGGAGCAGAAGCAGAACCTGGTGCATGGCATCCTGCACTTCATCAAGCCC
TGCCATCATGTGCTGAGCCTGTCCTTCCACATCCGGCATGACGACAGCTCCTGGGAAGTCATTGAGGGCTACTGGGCCCA
GCACAGCCAGCACCGCATGCCCTGCAAGGAAGGTATCCATTATAGCACTGATGTGAGTGTAGATAAAGTTAAAGCTCTGG
CTTATCTGATAACATATAAGTGTGCAGTGGTTGATGTGCCATTTAGGGTTGTCAAAGCTGATGTTTAGGTCAATCCCAAG
CACTATACTGATAATGAATTGGAAAAGATCACAAGGAGGTTCACCATGGAGCTGGCAAGAAGGGCTTTATTGGTCCTGGC
ATTGATGCGCCTGCCCCAGACATGAGCACAGGCCAACTGGAGATGTCCTGGATTGCTGACACCCATGGTAGCACTATAGG
GCACTCTGGTGTTAATGCCCATACCTGTATTACCAGTAAGCCCATCAGTCAGCATGGAATCCACAGACGGATCTCTGCTA
CTGGTCAGGGAGTTTTCCATGGAATTGAAAACTGCATCAATGAATCTTCTTACATGAGTATTTTAGGAATGACACCAGGA
TTTGGAGATAAAACATTTGCCGTTCAGGGATTTGGCAATGTGAGCCTGTACTCTATGAGATATTTACATCGTTTTCGTGC
TAAATGTGTTGCTGTTTGTGAGTCTGATGACAGCATATGGAATCCAGATAGTATTGAACAAAAGGAACTGGAATACTTCA
AATTGCAACATGAAACAATCCTGGGCTTCCCCAAAGCAAAGATCTATGAAAGGAGAATCTTGGAGGTTGACTGTGACATC
CCTGCTGCCAGCGAAAAGCAGCTGACCAAGTCCAATGCACCAAGAGTCAAAGCCAAGATCATTGCTGAAGGTGCCAATGG
ACCAACAACTCCAGAAGCTGATAAGATTTTGCTAGAGAGAAACATCATGGTTTTTCCAGATCTCTACTTGAATGCTGGAG
TAGTGACAGTATTTTACTTTGAGTAGCTAAAGAATTGAAATCATGTCAGCTATGGCCATTTGAACTTCAAATATGAAAGG
GATTCTAACTACCACTTGCTCATGTTTGTTCAAGAGAGTTTGGAAAGGAAATTTGGAAAATATGGTGGAACTATTCCTTA
TTGTACCTACAGCAGAGTTCCAAGACTGGATATCTGACAAAGACATTGTGCACTCTGGCTTAGCTACACCATGGAGCACC
CTGCCAGGCAAATCATGCACACAGTCATGAAATGTAACCTGGGATTGGACCTGAGAACAGCTGCCTATGTCAACACCATT
GAGAAAGTCTTCAAGGTGTACAATGAAGCTGGTGTGACCTTCACA

ORF - retro_btau_1741 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 81.89 %
Parental protein coverage: 93.94 %
Number of stop codons detected: 4
Number of frameshifts detected: 3


Retrocopy - Parental Gene Alignment:

ParentalGQAAAAVAAPQPGLVPPARRHYSEAAADREDDPNFFKMVEGFFDRGASIVEDKLVEDLKTRETEEQKRNR
GQ.AAA..A.QPGLVP.A..HYSE..A..EDD..FF.MVEGFFDR.ASI.EDKLVEDLKT.ETEEQK.N.
RetrocopyGQHAAAISALQPGLVPSAQ*HYSEVVANCEDDLSFFNMVEGFFDRSASIMEDKLVEDLKTQETEEQKQNL
ParentalVRGILRIIKPCNHVLSLSFPIRRDDGSWEVIEGYRAQHSQHRTPCKGGIRYSTDVSVDEVKALASLMTYK
V.GIL..IKPC.HVLSLSF.IR.DD.SWEVIEGY.AQHSQHR.PCK.GI.YSTDVSVD.VKALA.L.TYK
RetrocopyVHGILHFIKPCHHVLSLSFHIRHDDSSWEVIEGYWAQHSQHRMPCKEGIHYSTDVSVDKVKALAYLITYK
ParentalCAVVDVPFGGAKAGVKINPKNYTDNELEKITRRFTMELA-KKGFIGPGVDVPAPDMSTGEREMSWIADTY
CAVVDVPF...KA.V..NPK.YTDNELEKITRRFTMELA.KKGFIGPG.D.PAPDMSTG..EMSWIADT.
RetrocopyCAVVDVPFRVVKADV*VNPKHYTDNELEKITRRFTMELA<KKGFIGPGIDAPAPDMSTGQLEMSWIADTH
ParentalASTIGHYDINAHACVTGKPISQGGIHGRISATGRGVFHGIENFINEASYMSILGMTPGFGDKTFAVQGFG
.STIGH...NAH.C.T.KPISQ.GIH.RISATG.GVFHGIEN.INE.SYMSILGMTPGFGDKTFAVQGFG
RetrocopyGSTIGHSGVNAHTCITSKPISQHGIHRRISATGQGVFHGIENCINESSYMSILGMTPGFGDKTFAVQGFG
ParentalNVGLHSMRYLHRFGAKCVAVGESDGSIWNPDGIDPKELEDFKLQHGTILGFPKAKIYEGSILEVDCDILI
NV.L.SMRYLHRF.AKCVAV.ESD.SIWNPD.I..KELE.FKLQH.TILGFPKAKIYE..ILEVDCD..I
RetrocopyNVSLYSMRYLHRFRAKCVAVCESDDSIWNPDSIEQKELEYFKLQHETILGFPKAKIYERRILEVDCD--I
ParentalPAASEKQLTKSNAPRVKAKIIAEGANGPTTPEADKIFLERNIMVIPDLYLNAGGVTVSYFEWLKNLNHVS
PAASEKQLTKSNAPRVKAKIIAEGANGPTTPEADKI.LERNIMV.PDLYLNAG.VTV.YFE.LKN.NHVS
RetrocopyPAASEKQLTKSNAPRVKAKIIAEGANGPTTPEADKILLERNIMVFPDLYLNAGVVTVFYFE*LKN*NHVS
ParentalYGRLTFKYERDSNYHLLMSVQESLERKFGKHGGTIP-IVPTAEFQDRISGASEKDIVHSGLA-YTMERSA
YG.L.FKYERDSNYHLLM.VQESLERKFGK.GGTIP.IVPTAEFQD.IS....KDIVHSGLA.YTME..A
RetrocopyYGHLNFKYERDSNYHLLMFVQESLERKFGKYGGTIP>IVPTAEFQDWIS---DKDIVHSGLA<YTMEHPA
ParentalRQIMRTAMKYNLGLDLRTAAYVNAIEKVFRVYNEAGVTFT
RQIM.T.MK.NLGLDLRTAAYVN.IEKVF.VYNEAGVTFT
RetrocopyRQIMHTVMKCNLGLDLRTAAYVNTIEKVFKVYNEAGVTFT

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
ERP005899_liver 0 .00 RPM 587 .87 RPM
ERP005899_muscle 0 .05 RPM 304 .01 RPM
SRP017611_brain 0 .00 RPM 299 .47 RPM
SRP017611_kidney 0 .12 RPM 649 .08 RPM
SRP017611_liver 0 .15 RPM 571 .37 RPM
SRP030211_testis 0 .00 RPM 28 .05 RPM

ChIP-Seq - click to see more details

Bos taurus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_btau_1741 retrocopy.

TSS - click to see more details

Bos taurus was not studied using FANTOM5 data.

Lab - click to see more details

retro_btau_1741 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_btau_1741 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 20 parental genes, and 28 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG00000007540 2 retrocopies
retro_btau_1413, retro_btau_1741 ,
Canis familiaris ENSCAFG000000160951 retrocopy
retro_cfam_747,
Choloepus hoffmanni ENSCHOG000000011011 retrocopy
retro_chof_2002,
Callithrix jacchus ENSCJAG000000116331 retrocopy
retro_cjac_2830,
Dipodomys ordii ENSDORG000000097671 retrocopy
retro_dord_400,
Equus caballus ENSECAG000000073712 retrocopies
retro_ecab_886, retro_ecab_919,
Echinops telfairi ENSETEG000000196382 retrocopies
retro_etel_141, retro_etel_2024,
Homo sapiens ENSG000001486721 retrocopy
retro_hsap_31,
Gorilla gorilla ENSGGOG000000157701 retrocopy
retro_ggor_2954,
Loxodonta africana ENSLAFG000000120591 retrocopy
retro_lafr_504,
Microcebus murinus ENSMICG000000165261 retrocopy
retro_mmur_524,
Monodelphis domestica ENSMODG000000027561 retrocopy
retro_mdom_124,
Nomascus leucogenys ENSNLEG000000116581 retrocopy
retro_nleu_36,
Otolemur garnettii ENSOGAG000000036411 retrocopy
retro_ogar_2757,
Procavia capensis ENSPCAG000000086621 retrocopy
retro_pcap_11,
Pongo abelii ENSPPYG000000028273 retrocopies
retro_pabe_3109, retro_pabe_3213, retro_pabe_79,
Pan troglodytes ENSPTRG000000027114 retrocopies
retro_ptro_3162, retro_ptro_3283, retro_ptro_3285, retro_ptro_3290,
Ictidomys tridecemlineatus ENSSTOG000000128431 retrocopy
retro_itri_737,
Tarsius syrichta ENSTSYG000000015781 retrocopy
retro_tsyr_313,
Tursiops truncatus ENSTTRG000000081451 retrocopy
retro_ttru_950,


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